NDPIReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.SubResolutionFormatReader
    - - loci.formats.in.MinimalTiffReader
      - loci.formats.in.BaseTiffReader
        
        loci.formats.in.NDPIReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
```
public class NDPIReader
extends BaseTiffReader
```
NDPIReader is the file format reader for Hamamatsu .ndpi files.

Field Summary

Fields
Modifier and Type	Field and Description
`private static int`	`BLUE_MULTIPLIER`
`private static int`	`BYTE_COUNT_HIGH_BYTES`
`private static int`	`CAPTURE_MODE`
`private static int`	`DEFAULT_GAMMA`
`private static int`	`EXPOSURE_RATIO`
`private static int`	`EXPOSURE_TIME`
`private static int`	`FILTER_SET_NAME`
`private static int`	`FIRMWARE_VERSION`
`private static int`	`FOCUS_OFFSET`
`private static int`	`FOCUS_POINT_REGIONS`
`private static int`	`FOCUS_TIME`
`private static int`	`FULLY_AUTO_FOCUS`
`private static int`	`GREEN_MULTIPLIER`
`private int`	`initializedPlane`
`private int`	`initializedSeries`
`private java.lang.String`	`instrumentModel`
`private static int`	`JPEG_QUALITY`
`private static int`	`LABEL_OBSCURED`
`private static int`	`LAMP_AGE`
`private java.lang.Double`	`magnification`
`private static int`	`MARKER_TAG`
`private static int`	`MARKER_TAG_HIGH_BYTES`
`private static int`	`MAX_SIZE`
`private static int`	`METADATA_TAG`
`private static int`	`OFFSET_HIGH_BYTES`
`private int`	`pyramidHeight`
`private static int`	`RED_MULTIPLIER`
`private static int`	`REFERENCE`
`private static int`	`REFOCUS_INTERVAL`
`private static int`	`SCAN_TIME`
`private static int`	`SERIAL_NUMBER`
`private java.lang.String`	`serialNumber`
`private JPEGTurboService`	`service`
`private int`	`sizeZ`
`private static int`	`SOURCE_LENS`
`private static int`	`THUMB_TAG_2`
`private static int`	`TISSUE_INDEX`
`private static int`	`VERSION`
`private static int`	`WAVELENGTH`
`private static int`	`WRITE_TIME`
`private static int`	`X_POSITION`
`private static int`	`Y_POSITION`
`private static int`	`Z_POSITION`

Fields inherited from class loci.formats.in.BaseTiffReader
DATE_FORMATS, LOGGER

Fields inherited from class loci.formats.in.MinimalTiffReader
canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

Fields inherited from class loci.formats.SubResolutionFormatReader
core

Fields inherited from class loci.formats.FormatReader
coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler
COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description

NDPIReader()
Constructs a new NDPI reader.

Constructors
Constructor and Description
`NDPIReader()` Constructs a new NDPI reader.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close(boolean fileOnly)` Closes the currently open file.
`int`	`fileGroupOption(java.lang.String id)` Returns an indication of whether the files in a multi-file dataset can be handled individually.
`private int`	`getBitsPerSample(int mode)` Get the number of bits per sample associated with the given capture mode.
`private java.lang.String`	`getCaptureMode(int mode)` Get the description of the given capture mode.
`private int`	`getIFDIndex(int seriesIndex, int zIndex)`
`private long[]`	`getMarkers(IFD ifd)` Get the array of restart markers (offsets) for the given IFD.
`int`	`getOptimalTileHeight()` Returns the optimal sub-image height for use with openBytes.
`int`	`getOptimalTileWidth()` Returns the optimal sub-image width for use with openBytes.
`Codec`	`getTileCodec(int no)` Retrieve a codec that can be used to decompress compressed tiles.
`CodecOptions`	`getTileCodecOptions(int no, int x, int y)` Retrieve codec options that can be used to decompressed the specified tile.
`int`	`getTileColumns(int no)` Get the number of columns of tiles in the specified plane in the current series.
`int`	`getTileRows(int no)` Get the number of rows of tiles in the specified plane in the current series.
`protected void`	`initFile(java.lang.String id)` Initializes the given file (parsing header information, etc.).
`protected void`	`initMetadataStore()` Populates the metadata store using the data parsed in `BaseTiffReader.initStandardMetadata()` along with some further parsing done in the method itself.
`protected void`	`initStandardMetadata()` Parses standard metadata.
`boolean`	`isThisType(java.lang.String name, boolean open)` Checks if a file matches the type of this format reader.
`byte[]`	`openBytes(int no, byte[] buf, int x, int y, int w, int h)` Obtains a sub-image of the specified image plane into a pre-allocated byte array.
`byte[]`	`openCompressedBytes(int no, byte[] buf, int x, int y)` Retrieve the specified tile without performing any decompression.
`byte[]`	`openCompressedBytes(int no, int x, int y)` Retrieve the specified tile without performing any decompression.
`byte[]`	`openThumbBytes(int no)` Obtains a thumbnail for the specified image plane from the current file, as a byte array.
`private void`	`resetStream(IFD ifd)`
`private boolean`	`useTiffParser(IFD ifd)`

Methods inherited from class loci.formats.in.BaseTiffReader
getExifTagName, getImageCreationDate, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader
copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initTiffParser, isThisType, reopenFile, setResolutionLevel

Methods inherited from class loci.formats.SubResolutionFormatReader
coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

Methods inherited from class loci.formats.FormatReader
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.IFormatHandler
getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

- Field Detail
  - MAX_SIZE
```
private static final int MAX_SIZE
```
    See Also:
    
    Constant Field Values
  - OFFSET_HIGH_BYTES
```
private static final int OFFSET_HIGH_BYTES
```
    See Also:
    
    Constant Field Values
  - BYTE_COUNT_HIGH_BYTES
```
private static final int BYTE_COUNT_HIGH_BYTES
```
    See Also:
    
    Constant Field Values
  - VERSION
```
private static final int VERSION
```
    See Also:
    
    Constant Field Values
  - SOURCE_LENS
```
private static final int SOURCE_LENS
```
    See Also:
    
    Constant Field Values
  - X_POSITION
```
private static final int X_POSITION
```
    See Also:
    
    Constant Field Values
  - Y_POSITION
```
private static final int Y_POSITION
```
    See Also:
    
    Constant Field Values
  - Z_POSITION
```
private static final int Z_POSITION
```
    See Also:
    
    Constant Field Values
  - TISSUE_INDEX
```
private static final int TISSUE_INDEX
```
    See Also:
    
    Constant Field Values
  - MARKER_TAG
```
private static final int MARKER_TAG
```
    See Also:
    
    Constant Field Values
  - REFERENCE
```
private static final int REFERENCE
```
    See Also:
    
    Constant Field Values
  - MARKER_TAG_HIGH_BYTES
```
private static final int MARKER_TAG_HIGH_BYTES
```
    See Also:
    
    Constant Field Values
  - FILTER_SET_NAME
```
private static final int FILTER_SET_NAME
```
    See Also:
    
    Constant Field Values
  - EXPOSURE_RATIO
```
private static final int EXPOSURE_RATIO
```
    See Also:
    
    Constant Field Values
  - RED_MULTIPLIER
```
private static final int RED_MULTIPLIER
```
    See Also:
    
    Constant Field Values
  - GREEN_MULTIPLIER
```
private static final int GREEN_MULTIPLIER
```
    See Also:
    
    Constant Field Values
  - BLUE_MULTIPLIER
```
private static final int BLUE_MULTIPLIER
```
    See Also:
    
    Constant Field Values
  - THUMB_TAG_2
```
private static final int THUMB_TAG_2
```
    See Also:
    
    Constant Field Values
  - FOCUS_POINT_REGIONS
```
private static final int FOCUS_POINT_REGIONS
```
    See Also:
    
    Constant Field Values
  - CAPTURE_MODE
```
private static final int CAPTURE_MODE
```
    See Also:
    
    Constant Field Values
  - SERIAL_NUMBER
```
private static final int SERIAL_NUMBER
```
    See Also:
    
    Constant Field Values
  - JPEG_QUALITY
```
private static final int JPEG_QUALITY
```
    See Also:
    
    Constant Field Values
  - REFOCUS_INTERVAL
```
private static final int REFOCUS_INTERVAL
```
    See Also:
    
    Constant Field Values
  - FOCUS_OFFSET
```
private static final int FOCUS_OFFSET
```
    See Also:
    
    Constant Field Values
  - FIRMWARE_VERSION
```
private static final int FIRMWARE_VERSION
```
    See Also:
    
    Constant Field Values
  - METADATA_TAG
```
private static final int METADATA_TAG
```
    See Also:
    
    Constant Field Values
  - LABEL_OBSCURED
```
private static final int LABEL_OBSCURED
```
    See Also:
    
    Constant Field Values
  - WAVELENGTH
```
private static final int WAVELENGTH
```
    See Also:
    
    Constant Field Values
  - LAMP_AGE
```
private static final int LAMP_AGE
```
    See Also:
    
    Constant Field Values
  - EXPOSURE_TIME
```
private static final int EXPOSURE_TIME
```
    See Also:
    
    Constant Field Values
  - FOCUS_TIME
```
private static final int FOCUS_TIME
```
    See Also:
    
    Constant Field Values
  - SCAN_TIME
```
private static final int SCAN_TIME
```
    See Also:
    
    Constant Field Values
  - WRITE_TIME
```
private static final int WRITE_TIME
```
    See Also:
    
    Constant Field Values
  - FULLY_AUTO_FOCUS
```
private static final int FULLY_AUTO_FOCUS
```
    See Also:
    
    Constant Field Values
  - DEFAULT_GAMMA
```
private static final int DEFAULT_GAMMA
```
    See Also:
    
    Constant Field Values
  - initializedSeries
```
private int initializedSeries
```
  - initializedPlane
```
private int initializedPlane
```
  - sizeZ
```
private int sizeZ
```
  - pyramidHeight
```
private int pyramidHeight
```
  - service
```
private JPEGTurboService service
```
  - magnification
```
private java.lang.Double magnification
```
  - serialNumber
```
private java.lang.String serialNumber
```
  - instrumentModel
```
private java.lang.String instrumentModel
```
- Constructor Detail
  - NDPIReader
```
public NDPIReader()
```
    Constructs a new NDPI reader.
- Method Detail
  - getTileRows
```
public int getTileRows(int no)
```
    Description copied from interface: ICompressedTileReader
    
    Get the number of rows of tiles in the specified plane in the current series.
    
    Specified by:
    
    getTileRows in interface ICompressedTileReader
    
    Overrides:
    
    getTileRows in class FormatReader
    
    Parameters:
    
    no - plane index
    
    Returns:
    
    tile row count
  - getTileColumns
```
public int getTileColumns(int no)
```
    Description copied from interface: ICompressedTileReader
    
    Get the number of columns of tiles in the specified plane in the current series.
    
    Specified by:
    
    getTileColumns in interface ICompressedTileReader
    
    Overrides:
    
    getTileColumns in class FormatReader
    
    Parameters:
    
    no - plane index
    
    Returns:
    
    tile column count
  - openCompressedBytes
```
public byte[] openCompressedBytes(int no,
                                  int x,
                                  int y)
                           throws FormatException,
                                  java.io.IOException
```
    Description copied from interface: ICompressedTileReader
    
    Retrieve the specified tile without performing any decompression.
    
    Parameters:
    
    no - plane index
    
    x - tile X index (indexed from 0, @see getTileColumns(int))
    
    y - tile Y index (indexed from 0, @see getTileRows(int))
    
    Returns:
    
    compressed tile bytes
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - openCompressedBytes
```
public byte[] openCompressedBytes(int no,
                                  byte[] buf,
                                  int x,
                                  int y)
                           throws FormatException,
                                  java.io.IOException
```
    Description copied from interface: ICompressedTileReader
    
    Retrieve the specified tile without performing any decompression.
    
    Parameters:
    
    no - plane index
    
    buf - pre-allocated buffer in which to store compressed bytes
    
    x - tile X index (indexed from 0, @see getTileColumns(int))
    
    y - tile Y index (indexed from 0, @see getTileRows(int))
    
    Returns:
    
    compressed tile bytes
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getTileCodec
```
public Codec getTileCodec(int no)
                   throws FormatException,
                          java.io.IOException
```
    Description copied from interface: ICompressedTileReader
    
    Retrieve a codec that can be used to decompress compressed tiles.
    
    Parameters:
    
    no - plane index
    
    Returns:
    
    codec that can be used for compressed tiles in the specified plane
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    ICompressedTileReader.openCompressedBytes(int, int, int)
  - getTileCodecOptions
```
public CodecOptions getTileCodecOptions(int no,
                                        int x,
                                        int y)
                                 throws FormatException,
                                        java.io.IOException
```
    Description copied from interface: ICompressedTileReader
    
    Retrieve codec options that can be used to decompressed the specified tile.
    
    Parameters:
    
    no - plane index
    
    x - tile X index (indexed from 0, @see getTileColumns(int))
    
    y - tile Y index (indexed from 0, @see getTileRows(int))
    
    Returns:
    
    codec options
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    ICompressedTileReader.getTileCodec(int)
  - isThisType
```
public boolean isThisType(java.lang.String name,
                          boolean open)
```
    Description copied from class: FormatReader
    
    Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    Overrides:
    
    isThisType in class FormatReader
    
    open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.
  - fileGroupOption
```
public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.
    
    Specified by:
    
    fileGroupOption in interface IFormatReader
    
    Overrides:
    
    fileGroupOption in class FormatReader
    
    Parameters:
    
    id - a file in the multi-file dataset
    
    Returns:
    
    an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).
    
    Throws:
    
    FormatException
    
    java.io.IOException
    
    See Also:
    
    IFormatReader.fileGroupOption(String)
  - openBytes
```
public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Obtains a sub-image of the specified image plane into a pre-allocated byte array.
    
    Specified by:
    
    openBytes in interface IFormatReader
    
    Overrides:
    
    openBytes in class MinimalTiffReader
    
    Parameters:
    
    no - the plane index within the current series.
    
    buf - a pre-allocated buffer.
    
    x - X coordinate of the upper-left corner of the sub-image
    
    y - Y coordinate of the upper-left corner of the sub-image
    
    w - width of the sub-image
    
    h - height of the sub-image
    
    Returns:
    
    the pre-allocated buffer buf for convenience.
    
    Throws:
    
    FormatException - if there was a problem parsing the metadata of the file.
    
    java.io.IOException - if there was a problem reading the file.
    
    See Also:
    
    IFormatReader.openBytes(int, byte[], int, int, int, int)
  - openThumbBytes
```
public byte[] openThumbBytes(int no)
                      throws FormatException,
                             java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Obtains a thumbnail for the specified image plane from the current file, as a byte array.
    
    Specified by:
    
    openThumbBytes in interface IFormatReader
    
    Overrides:
    
    openThumbBytes in class MinimalTiffReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - close
```
public void close(boolean fileOnly)
           throws java.io.IOException
```
    Description copied from interface: IFormatReader
    
    Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().
    
    Specified by:
    
    close in interface IFormatReader
    
    Overrides:
    
    close in class MinimalTiffReader
    
    Throws:
    
    java.io.IOException
  - getOptimalTileWidth
```
public int getOptimalTileWidth()
```
    Description copied from interface: IFormatReader
    
    Returns the optimal sub-image width for use with openBytes.
    
    Specified by:
    
    getOptimalTileWidth in interface IFormatReader
    
    Overrides:
    
    getOptimalTileWidth in class MinimalTiffReader
  - getOptimalTileHeight
```
public int getOptimalTileHeight()
```
    Description copied from interface: IFormatReader
    
    Returns the optimal sub-image height for use with openBytes.
    
    Specified by:
    
    getOptimalTileHeight in interface IFormatReader
    
    Overrides:
    
    getOptimalTileHeight in class MinimalTiffReader
  - initFile
```
protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException
```
    Description copied from class: SubResolutionFormatReader
    
    Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.
    
    Overrides:
    
    initFile in class BaseTiffReader
    
    Throws:
    
    FormatException - if a parsing error occurs processing the file.
    
    java.io.IOException - if an I/O error occurs processing the file
  - initStandardMetadata
```
protected void initStandardMetadata()
                             throws FormatException,
                                    java.io.IOException
```
    Description copied from class: BaseTiffReader
    
    Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.
    
    Overrides:
    
    initStandardMetadata in class BaseTiffReader
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - initMetadataStore
```
protected void initMetadataStore()
                          throws FormatException
```
    Description copied from class: BaseTiffReader
    
    Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself. All calls to the active MetadataStore should be made in this method and only in this method. This is especially important for sub-classes that override the getters for pixel set array size, etc.
    
    Overrides:
    
    initMetadataStore in class BaseTiffReader
    
    Throws:
    
    FormatException
  - getIFDIndex
```
private int getIFDIndex(int seriesIndex,
                        int zIndex)
```
  - useTiffParser
```
private boolean useTiffParser(IFD ifd)
                       throws FormatException
```
    Returns:
    
    true if tiles can be read using TiffParser logic, or false if the JPEGTurboService needs to be used
    
    Throws:
    
    FormatException
  - getCaptureMode
```
private java.lang.String getCaptureMode(int mode)
```
    Get the description of the given capture mode.
  - getBitsPerSample
```
private int getBitsPerSample(int mode)
```
    Get the number of bits per sample associated with the given capture mode.
  - getMarkers
```
private long[] getMarkers(IFD ifd)
                   throws FormatException
```
    Get the array of restart markers (offsets) for the given IFD. Reads both the marker tag and marker high bytes tag (if present) to build the array of 64-bit offsets.
    
    Throws:
    
    FormatException
  - resetStream
```
private void resetStream(IFD ifd)
                  throws java.io.IOException,
                         FormatException
```
    Throws:
    
    java.io.IOException
    
    FormatException

Class NDPIReader

Field Summary

Fields inherited from class loci.formats.in.BaseTiffReader

Fields inherited from class loci.formats.in.MinimalTiffReader

Fields inherited from class loci.formats.SubResolutionFormatReader

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.in.BaseTiffReader

Methods inherited from class loci.formats.in.MinimalTiffReader

Methods inherited from class loci.formats.SubResolutionFormatReader

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Methods inherited from interface loci.formats.IMetadataConfigurable

Field Detail

MAX_SIZE

OFFSET_HIGH_BYTES

BYTE_COUNT_HIGH_BYTES

VERSION

SOURCE_LENS

X_POSITION

Y_POSITION

Z_POSITION

TISSUE_INDEX

MARKER_TAG

REFERENCE

MARKER_TAG_HIGH_BYTES

FILTER_SET_NAME

EXPOSURE_RATIO

RED_MULTIPLIER

GREEN_MULTIPLIER

BLUE_MULTIPLIER

THUMB_TAG_2

FOCUS_POINT_REGIONS

CAPTURE_MODE

SERIAL_NUMBER

JPEG_QUALITY

REFOCUS_INTERVAL

FOCUS_OFFSET

FIRMWARE_VERSION

METADATA_TAG

LABEL_OBSCURED

WAVELENGTH

LAMP_AGE

EXPOSURE_TIME

FOCUS_TIME

SCAN_TIME

WRITE_TIME

FULLY_AUTO_FOCUS

DEFAULT_GAMMA

initializedSeries

initializedPlane

sizeZ

pyramidHeight

service

magnification

serialNumber

instrumentModel

Constructor Detail

NDPIReader

Method Detail

getTileRows

getTileColumns

openCompressedBytes

openCompressedBytes

getTileCodec

getTileCodecOptions

isThisType

fileGroupOption

openBytes

openThumbBytes

close

getOptimalTileWidth

getOptimalTileHeight

initFile

initStandardMetadata